Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Neural
Cell type
LN-229
Primary Tissue
Brain
Tissue Diagnosis
Glioma

Attributes by original data submitter

Sample

source_name
tumorigenic adherent glioma cell line (LN229)
cell type
tumorigenic adherent glioma cell line (LN229)
chip antibody
CTCF (#3418, Cell Signaling)
treatment
Treated with CrispR Cas9 LINC01116 (enhancer) sgRNA

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7546S, NEB). ChIP-Seq with Drosophila spike-in chromatin (Cat. 53083, Active Motif) and Drosophila -specific histone variant, H2Av (Cat. 61686, Active Motif) were added to each sample prior IP for normalization.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
9829685
Reads aligned (%)
98.4
Duplicates removed (%)
1.9
Number of peaks
1971 (qval < 1E-05)

hg19

Number of total reads
9829685
Reads aligned (%)
98.0
Duplicates removed (%)
2.9
Number of peaks
2058 (qval < 1E-05)

Base call quality data from DBCLS SRA